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Table 2 Assembly statistics

From: Genomic factors related to tissue tropism in Chlamydia pneumoniae infection

    Filtering   Mapping   Comparative assembly
Isolate Read length Total seq. (Mb) Passed filtering (Mb) Passed filtering % Filter criterion Chlamydial reference isolate Mapped total (Mb) Mapped to human (Mb) Mapped to Chlamydia (Mb) Chlamydia reference coverage % Total for comp. assembly (Mb) # Contigs Total assembled nucleotides Average coverage
CM1 76 2561 1827.9 71.38% qual, l36 AR39 1662.3 1518.7 143.6 99.9% 309 1 1,229,887 147.0
CV14 74 2094 1747.1 83.44% qual, l36, mp CWL029 1703.1 1440.5 262.6 99.9% 307 1 1,228,123 243.0
CV15 36 624 602.0 96.47% qual, l30 CWL029 498.3 388.9 109.5 99.9% 213 3 1,228,165 86.5
CWL011 76 3061 2040.3 66.65% qual, l36 CWL029 1954.2 1876.8 77.4 99.9% 163 1 1,228,579 58.3
CWL029c 36 556 545.3 98.07% qual, l30, mp CWL029 532.1 463.5 68.6 99.8% 82 7 1,228,575 56.0
DC9 74 1919 1724.6 89.87% qual, l36, mp CWL029 1640.8 1511.1 129.7 97.5% 214 85 1,214,883 111.6
GiD 76 1772 1675.8 94.57% qual, l36, mp AR39 1610.4 20.8 1589.6 99.9% 1655 2 1,229,850 1,334.6
H12 76 294 259.0 88.11% qual, l36, mp CWL029 248.8 233.2 15.7 93.7% 26 147 1,224,589 12.9
K7 74 2344 2137.0 91.17% qual, l36, mp CWL029 2076.6 1847.3 229.3 99.9% 290 1 1,228,523 195.2
MUL2216 36 520 510.3 98.14% qual, l30, mp CWL029 467.6 420.8 46.8 99.8% 90 7 1,228,567 38.2
Panola 54 1025 912.0 88.98% qual, l36, mp CWL029 881.9 837.3 44.6 99.7% 75 13 1,228,514 38.5
PB1 36 464 457.1 98.51% qual, l30, mp CWL029 446.4 302.1 144.3 99.9% 155 2 1,228,135 113.2
PB2 74 1806 1612.0 89.26% qual, l36, mp CWL029 1564.9 1338.2 226.6 99.9% 274 2 1,228,201 195.5
U1271 74 1623 1494.5 92.08% qual, l36, mp CWL029 1462.7 1351.4 111.3 99.9% 143 3 1,228,567 93.9
UZG1 36 472 464.6 98.43% qual, l30, mp TW183 389.3 325.1 64.2 99.7% 139 3 1,225,933 52.7
Wien1 76 1241 1150.2 92.68% qual, l36, mp CWL029 1120.5 885.5 235.0 99.9% 265 1 1,228,125 195.5
Wien2 74 1955 1784.7 91.29% qual, l36, mp CWL029 1722.1 1440.8 281.3 99.8% 344 9 1,228,526 237.8
Wien3 76 3223 1702.8 52.83% qual, l36 CWL029 1657.0 1344.6 312.4 99.9% 358 1 1,228,576 243.8
YK41 36 549 538.0 97.99% qual, l30, mp AR39 522.7 492.1 30.6 99.0% 46 61 1,229,406 25.0
  1. Summary statistics of the processing steps in the assembly of the sequenced isolates. Filter criteria were adjusted to each dataset (qual: quality trimming from 3′ end to a minimal Phred score of 20; l36: minimal read length after trimming of 36 nt; l30: minimal read length after trimming of 30 nt; mp: only paired reads).